Getting all the things you need:

Playing as the freighter

The freighter only gets points for carrying cargo from one of the ports in the south in the gulf to the ports in the north and visa versa.
All you need to do is making sure to rez the boat in a port, attach your Freighter Manifest HUD, select the destination and set sail. Oh, and make sure you don’t get blown up by a submarine.
As a freighter you can’t really defend yourself against submarines, so if you encounter resistance make sure to have a friend or someone else to get in a round table to escort you.

Playing as the escort

The escort is meant to escort freighters and protect them from submarines. Escorts rack up points by staying close to a freighter during the journey. Every few minutes it’ll get points.
You need to rez the round table in a port, attach your Combat Log HUD, say ‘lance on’ in local chat, make sure you’re the same team as the freighter (by clicking your boat and selecting the team) and set sail while sticking with the boat you’re escorting. You can only escort players, not NPCs.
You have depth charges to destroy submarines. It is vital that you set the right depth for them as damage scales more dramatically on distance on the depth/z-axis than it does on the left or right/x or y axis.

Playing as the submarine

The submarine solely gets points by destroying freighters. You get the points the freighter normally would get if it completed its journey.
You need to rez the submarine in a port, attach your Combat Log HUD, say ‘lance on’ in local chat and set sail to destroy some freighters with your torpedoes. To reload your torpedoes make sure to surface and stay still for 30 seconds.
You mostly need to fear the round tables. When you’re underwater freighters cannot damage you.

Playing as the air support

The escort is meant to hunt submarines and trawlers. Air support rack up points by shooting down trawlers and submarines.
You need to rez the support aircraft in a takeoff area, attach your Combat Log HUD, say ‘lance on’ in local chat and ‘team #’ to set a team.
You have depth charges to destroy submarines. It is vital that you set the right depth for them as damage scales more dramatically on distance on the depth/z-axis than it does on the left or right/x or y axis.